Align Ornithine aminotransferase; Orn-AT; Ornithine delta-aminotransferase; EC 2.6.1.13 (characterized)
to candidate 5208454 Shew_0966 beta alanine--pyruvate transaminase (RefSeq)
Query= SwissProt::O50131 (454 letters) >FitnessBrowser__PV4:5208454 Length = 446 Score = 182 bits (461), Expect = 2e-50 Identities = 136/441 (30%), Positives = 217/441 (49%), Gaps = 27/441 (6%) Query: 21 EHHKYMATTTNDPNEYFLVIERAEGVYWIDVDGNVLLDFSSGIGVMNVGLRNPKVIEAIK 80 EH+ T + ++ +AEG+Y+ DV+G +LD ++G+ N G + EA+ Sbjct: 16 EHYWMPFTANRQFKQSPRLLAQAEGMYYKDVNGRPVLDGTAGLWCCNAGHGRKAISEAVS 75 Query: 81 KQLDLVLHAAGTDYYNPYQVELAKKLVEIAPGDIERKVFLSNSGTEANEAALKIA----- 135 KQ+ + +A +P ELA++L IAP I KVF +NSG+E+ + ALKIA Sbjct: 76 KQIHEMDYAPSFQMGHPLAFELAERLAAIAPKGIN-KVFFTNSGSESVDTALKIALNYHR 134 Query: 136 -KWSTNRKMFIAFIGAFHGRTHGTMSLTASKPVQRSRMFPTMPGVVHVPYPNPYRNPWGI 194 + R FI +HG G +S+ +R+ + GV H+P+ + Sbjct: 135 ARGEATRTRFIGRELGYHGVGFGGISVGGIGGNRRTFSQQLLQGVDHLPHTLDIQQNAFC 194 Query: 195 DGYENPDELINRVIDYIEEYLFEHYVPAEEVAGIFFEPIQGEGGYVVPPKNFFKELKKLA 254 G E + +E+ + H AE +A + EP+ G G ++PP+ + K L+++ Sbjct: 195 KGLP---ETGAEKAEVLEQLVTLH--GAENIAAVIVEPMSGSAGVILPPQGYLKRLREIT 249 Query: 255 DKHGILLIDDEVQMGMGRTGRMWAIEHFDIVPDIVTVAKALGGG-IPIGA-----TIFRA 308 K+GILLI DEV G GR G +A + + + PD++T AKAL G IP+GA I+ A Sbjct: 250 RKYGILLIFDEVITGFGRVGDAFASQRWGVTPDMITTAKALNNGTIPMGAVLIDDAIYDA 309 Query: 309 DLDFGVSGV---HSNTFGGNTVAAAAALAVIEELQ-NGLIENAQKLEPLFRERLEEMKEK 364 +D + H T+ G+ VAAAAA+A ++ Q L E + LE F + + +K Sbjct: 310 SMDAPEGAIELYHGYTYSGHPVAAAAAIATLDIYQEEQLFERTKSLEGYFEKAVHSLKGL 369 Query: 365 YEIIGDVRGLGLAWGVEFVKDRKTKEYATKERGEIVVEALKRGLALLGCGKSAIRLIPPL 424 +I D+R GL G++F K +RG + E + L+ I L PPL Sbjct: 370 PNLI-DIRNTGLVAGIQFSPSDK----GIGKRGFGIFETCFKNGTLVRATADTIALSPPL 424 Query: 425 IISEEEAKMGLDIFEEAIKVV 445 I+ E + ++ +AI V Sbjct: 425 IVDEAQIDQMVNTLSDAITTV 445 Lambda K H 0.319 0.139 0.410 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 461 Number of extensions: 23 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 454 Length of database: 446 Length adjustment: 33 Effective length of query: 421 Effective length of database: 413 Effective search space: 173873 Effective search space used: 173873 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory